diff tool_dependencies.xml @ 3:52a70ef5248c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 568023f8019f928a6f335951806c0c4a03f21320

--- a/tool_dependencies.xml	Mon Jun 06 10:39:18 2016 -0400
+++ b/tool_dependencies.xml	Tue Jun 07 04:06:15 2016 -0400
@@ -1,15 +1,20 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="blast" version="2.2.22">
-        <repository changeset_revision="4f8b2f842678" name="package_legacy_blast_2_2_22" owner="saskia-hiltemann" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="boost" version="1.57">
-        <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />
-    </package>
     <package name="mothur" version="1.36.1">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://github.com/mothur/mothur/archive/v1.36.1.zip</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="4f8b2f842678" name="package_legacy_blast_2_2_22" owner="saskia-hiltemann" toolshed="testtoolshed.g2.bx.psu.edu">
+                        <package name="blast" version="2.2.22" />
+                    </repository>
+                    <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" toolshed="testtoolshed.g2.bx.psu.edu">
+                        <package name="boost" version="1.57" />
+                    </repository>
+                    <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="testtoolshed.g2.bx.psu.edu">
+                        <package name="zlib" version="1.2.8" />
+                    </repository>
+                </action>
                 <action type="shell_command">chmod u+x source/uchime_src/mk</action>
                 <action type="shell_command">
                     test $(uname) = Linux &amp;&amp;
@@ -19,7 +24,8 @@
                 <action type="shell_command">sed -i 's/\ \ \ \ /\t/g' source/makefile;</action>
                 <action type="shell_command">sed -i '141d;151d;152d' source/makefile;</action>
                 <action type="shell_command">sed -i 's/fortranSource//g' source/makefile;</action>
-                <action type="shell_command">sed -i 's/\/usr\/local/$BOOST_ROOT_DIR/g' source/makefile;</action>
+                <action type="shell_command">sed -i 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile;</action>
+                <action type="shell_command">ln -s ${ZLIB_ROOT_DIR}/zlib.a ${BOOST_ROOT_DIR}/boost/lib/</action>
 
                 <action type="shell_command">cd source; make -j 2;</action>
                 <action type="move_file">
@@ -32,15 +38,6 @@
                 </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="MOTHUR_MAX_PROCESSORS">2</environment_variable>
-                </action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="4f8b2f842678" name="package_legacy_blast_2_2_22" owner="saskia-hiltemann" toolshed="testtoolshed.g2.bx.psu.edu">
-                        <package name="blast" version="2.2.22" />
-                    </repository>
-                    <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="boost" version="1.57" />
-                    </repository>
                 </action>
                 <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
                 <action type="change_directory">$INSTALL_DIR/bin</action>
@@ -73,5 +70,14 @@
 - libncurses-dev(el)
 - simplejson (python library)
         </readme>
-    </package>
+        </package>
+        <package name="blast" version="2.2.22">
+            <repository changeset_revision="4f8b2f842678" name="package_legacy_blast_2_2_22" owner="saskia-hiltemann" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="boost" version="1.57">
+            <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="zlib" version="1.2.8">
+            <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />
+        </package>
 </tool_dependency>